Phylogenomics and the diversity and the diversification of microbes

Phylogenomics and the Diversity and Diversification of Microbes

Jonathan A. EisenUC Davis

Calacademy TalkDecember 16, 2010

1Monday, November 26, 12

Phylogenomics of Novelty

Origin of New Functions and

Processes

Species Evolution

Genome Dynamics

•New genes•Changes in old genes•Changes in pathways

•Phylogenetic history•Vertical vs. horizontal descent•Needed to track gain/loss of processes, infer convergence

•Evolvability•Repair and recombination processes•Intragenomic variation

Monday, November 26, 12

Phylogenomic Analysis

• Evolutionary reconstructions greatly improve genome analyses

• Genome analysis greatly improves evolutionary reconstructions

• There is a feedback loop such that these should be integrated


Outline

• Introduction• Phylogenomic Tales

– Selecting genomes for sequencing– Species evolution– Predicting functions of genes– Uncultured microbes


Outline

• Introductino• Phylogenomic Tales

– Selecting genomes for sequencing– Species evolution– Predicting functions of genes– Uncultured microbes

• All of these going to be told in context of a recent project “A Genomic Encyclopedia of Bacteria and Archaea” (aka GEBA)


Fleischmann et al. 1995 6


Whole Genome Shotgun Sequencing





Warner Brothers, Inc.



shotgun




shotgun




shotgun

sequenceWarner Brothers, Inc.



shotgun

sequenceWarner Brothers, Inc.


Assemble Fragments


Assemble Fragments

sequencer output


Assemble Fragments

sequencer output


Assemble Fragments

sequencer output

assemble fragments


Assemble Fragments

sequencer output

assemble fragments

Closure &

Annotation


From http://genomesonline.org 9Monday, November 26, 12




Human commensals


Genome Sequences Have Revolutionized Microbiology

• Predictions of metabolic processes

• Better vaccine and drug design

• New insights into mechanisms of evolution

• Genomes serve as template for functional studies

• New enzymes and materials for engineering and synthetic biology


From http://genomesonline.org 15Monday, November 26, 12

rRNA Tree of Life

FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.

Based on tree from Pace NR, 2003.

Archaea

Eukaryotes

Bacteria


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

As of 2002

Based on Hugenholtz, 2002 17


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Genome sequences are mostly from three phyla

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter



• Some other phyla are only sparsely sampled

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




Based on Hugenholtz, 2002

2002


Need for Tree Guidance Well Established

• Common approach within some eukaryotic groups

• Many small projects funded to fill in some bacterial or archaeal gaps

• Phylogenetic gaps in bacterial and archaeal projects commonly lamented in literature


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Solution I: sequence more phyla

• NSF-funded Tree of Life Project

• A genome from each of eight phyla

Eisen & Ward, PIs22


Phylum

Species selected

Chrysiogenes

Chrysiogenes arsenatis (GCA)

Coprothermobacter

Coprothermobacter proteolyticus (GCBP)

Dictyoglomi

Dictyoglomus thermophilum (GD T )

Thermodesulfobacteria

Thermodesulfobacterium commune (GTC)

Nitrospirae

Thermodesulfovibrio yellowstonii (GTY)

Thermomicrobia

Thermomicrobium roseum (GTR )

Deferribacteres

Geovibrio thiophilus (GGT)

Synergistes

Synergistes jonesii (GSJ)

Organisms Selected


Bacterial aTOL Project AIMS

• Improve resolution of deep branches in the bacterial tree

• Launch biological studies of these phyla

• Leverage data for interpreting environmental surveys



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Still highly biased in terms of the tree



Eisen & Ward, PIs


Major Lineages of Actinobacteria2.5.1 Acidimicrobidae2.5.1.1 Unclassified2.5.1.2 "Microthrixineae2.5.1.3 Acidimicrobineae2.5.1.4 BD2-102.5.1.5 EB10172.5.2 Actinobacteridae2.5.2.1 Unclassified2.5.2.10 Ellin306/WR1602.5.2.11 Ellin50122.5.2.12 Ellin50342.5.2.13 Frankineae2.5.2.14 Glycomyces2.5.2.15 Intrasporangiaceae2.5.2.16 Kineosporiaceae2.5.2.17 Microbacteriaceae2.5.2.18 Micrococcaceae2.5.2.19 Micromonosporaceae2.5.2.2 Actinomyces2.5.2.20 Propionibacterineae2.5.2.21 Pseudonocardiaceae2.5.2.22 Streptomycineae2.5.2.23 Streptosporangineae2.5.2.3 Actinomycineae2.5.2.4 Actinosynnemataceae2.5.2.5 Bifidobacteriaceae2.5.2.6 Brevibacteriaceae2.5.2.7 Cellulomonadaceae2.5.2.8 Corynebacterineae2.5.2.9 Dermabacteraceae2.5.3 Coriobacteridae2.5.3.1 Unclassified2.5.3.2 Atopobiales2.5.3.3 Coriobacteriales2.5.3.4 Eggerthellales2.5.4 OPB412.5.5 PK12.5.6 Rubrobacteridae2.5.6.1 Unclassified2.5.6.2 "Thermoleiphilaceae2.5.6.3 MC472.5.6.4 Rubrobacteraceae

2.5 Actinobacteria2.5.1 Acidimicrobidae2.5.1.1 Unclassified2.5.1.2 "Microthrixineae2.5.1.3 Acidimicrobineae2.5.1.3.1 Unclassified2.5.1.3.2 Acidimicrobiaceae2.5.1.4 BD2-102.5.1.5 EB10172.5.2 Actinobacteridae2.5.2.1 Unclassified2.5.2.10 Ellin306/WR1602.5.2.11 Ellin50122.5.2.12 Ellin50342.5.2.13 Frankineae2.5.2.13.1 Unclassified2.5.2.13.2 Acidothermaceae2.5.2.13.3 Ellin60902.5.2.13.4 Frankiaceae2.5.2.13.5 Geodermatophilaceae2.5.2.13.6 Microsphaeraceae2.5.2.13.7 Sporichthyaceae2.5.2.14 Glycomyces2.5.2.15 Intrasporangiaceae2.5.2.15.1 Unclassified2.5.2.15.2 Dermacoccus2.5.2.15.3 Intrasporangiaceae2.5.2.16 Kineosporiaceae2.5.2.17 Microbacteriaceae2.5.2.17.1 Unclassified2.5.2.17.2 Agrococcus2.5.2.17.3 Agromyces2.5.2.18 Micrococcaceae2.5.2.19 Micromonosporaceae2.5.2.2 Actinomyces2.5.2.20 Propionibacterineae2.5.2.20.1 Unclassified2.5.2.20.2 Kribbella2.5.2.20.3 Nocardioidaceae2.5.2.20.4 Propionibacteriaceae2.5.2.21 Pseudonocardiaceae2.5.2.22 Streptomycineae2.5.2.22.1 Unclassified2.5.2.22.2 Kitasatospora2.5.2.22.3 Streptacidiphilus2.5.2.23 Streptosporangineae2.5.2.23.1 Unclassified2.5.2.23.2 Ellin51292.5.2.23.3 Nocardiopsaceae2.5.2.23.4 Streptosporangiaceae2.5.2.23.5 Thermomonosporaceae2.5.2.3 Actinomycineae2.5.2.4 Actinosynnemataceae2.5.2.5 Bifidobacteriaceae2.5.2.6 Brevibacteriaceae2.5.2.7 Cellulomonadaceae2.5.2.8 Corynebacterineae2.5.2.8.1 Unclassified2.5.2.8.2 Corynebacteriaceae2.5.2.8.3 Dietziaceae2.5.2.8.4 Gordoniaceae2.5.2.8.5 Mycobacteriaceae2.5.2.8.6 Rhodococcus2.5.2.8.7 Rhodococcus2.5.2.8.8 Rhodococcus2.5.2.9 Dermabacteraceae2.5.2.9.1 Unclassified2.5.2.9.2 Brachybacterium2.5.2.9.3 Dermabacter2.5.3 Coriobacteridae2.5.3.1 Unclassified2.5.3.2 Atopobiales2.5.3.3 Coriobacteriales2.5.3.4 Eggerthellales2.5.4 OPB412.5.5 PK12.5.6 Rubrobacteridae2.5.6.1 Unclassified2.5.6.2 "Thermoleiphilaceae2.5.6.2.1 Unclassified2.5.6.2.2 Conexibacter2.5.6.2.3 XGE5142.5.6.3 MC472.5.6.4 Rubrobacteraceae


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Archaea



Eisen & Ward, PIs


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Eukaryotes



Eisen & Ward, PIs


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Viruses



Eisen & Ward, PIs





• Solution: Really Fill in the Tree

• GEBA• A genomic

encyclopedia of bacteria and archaea

Eisen & Ward, PIs

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


http://www.jgi.doe.gov/programs/GEBA/pilot.html 32Monday, November 26, 12

GEBA Pilot Project Overview

• Identify major branches in rRNA tree for which no genomes are available

• Identify those with a cultured representative in DSMZ

• DSMZ grew > 200 of these and prepped DNA• Sequence and finish 100+ (covering breadth of

bacterial/archaea diversity)• Annotate, analyze, release data• Assess benefits of tree guided sequencing• 1st paper Wu et al in Nature Dec 2009


GEBA Pilot Project: Components• Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan

Eisen, Eddy Rubin, Jim Bristow)• Project management (David Bruce, Eileen Dalin, Lynne Goodwin)• Culture collection and DNA prep (DSMZ, Hans-Peter Klenk)• Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus,

Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng)• Annotation and data release (Nikos Kyrpides, Victor Markowitz, et

al)• Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor

Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla)

• Adopt a microbe education project (Cheryl Kerfeld)• Outreach (David Gilbert)• $$$ (DOE, Eddy Rubin, Jim Bristow) 34


GEBA Phylogenomic Lesson 1

The rRNA Tree of Life is a Useful Tool for Identifying Phylogenetically Novel

Genomes


rRNA Tree of Life



Archaea

Eukaryotes

Bacteria


Network of Life

Figure from Barton, Eisen et al. “Evolution”, CSHL Press.


Archaea

Eukaryotes

Bacteria


“Whole Genome” Concatenation Tree w/ AMPHORA

http://bobcat.genomecenter.ucdavis.edu/AMPHORA/See Wu and Eisen, Genome Biology 2008 9: R151


http://bobcat.genomecenter.ucdavis.edu/AMPHORA/




Compare PD in Trees



PD of rRNA, Genome Trees Similar

From Wu et al. 2009 Nature 462, 1056-1060


http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html



rRNA Tree is good but not perfectand better genomic sampling improves

phylogenetic inference


16s Says Hyphomonas is in Rhodobacteriales

Badger et al. 2005


WGT and individual gene trees:Its Related to Caulobacterales

Badger et al. 2005



Phylogeny-driven genome selection helps discover new genetic diversity


Network of Life



Archaea

Eukaryotes

Bacteria


Protein Family Rarefaction Curves

• Take data set of multiple complete genomes• Identify all protein families using MCL• Plot # of genomes vs. # of protein families







Synapomorphies exist


Structural Novelty

• Of the 17000 protein families in the GEBA56, 1800 are novel in sequence (Wu)

• Structural modeling suggests many are structurally novel too (D'haeseleer)

• 372 being crystallized by the PSI (Kerfeld)


Phylogenetic Distribution Novelty: Bacterial Actin Related Protein

Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin

A. cliftonii gi14269497U. pertusa gi50355609

C. boidinii gi57157304S. cerevisiae gi14318479L. starkeyi gi166080363 S. japonicus gi213407080

H. sapiens gi4501889M. cerebralis gi46326807

C. cinerea gi169844021N. crassa gi85101929I. scapularis gi215507378 H. sapiens gi5031569

S. japonicus gi213404844S. cerevisiae gi6320175D. melanogaster gi24642545G. gallus gi45382569C. neoformans gi58266690S. cerevisiae gi6322525D. melanogaster gi17737543H. sapiens gi5031573 H. ochraceum gi227395998

P. patens gi168051992 A. thaliana gi18394608

S. cerevisiae gi1008244

D. melanogaster gi17737347

D. hansenii gi218511921S. cerevisiae gi6323114

S. japonicus gi213408393 S. cerevisiae gi1301932

D. discoideum gi66802418

O. sativa gi182657420 A. thaliana gi1841 1737

D. melanogater gi19920358M. musculus gi226246593

99

67

100100

65

100

100

75

100

100

51

9973

10097

94100

74

100

87

100

0.5

ACTIN

ARP1

ARP2

ARP3

BARP

ARP4

ARP5

ARP6

ARP7

ARP10

See also Guljamow et al. 2007 Current Biology.





Phylogeny driven genome selection (and phylogenetics in general) improves genome annotation


Predicting Function

• Key step in genome projects• More accurate predictions help guide

experimental and computational analyses• Many diverse approaches• All improved both by “phylogenomic” type

analyses that integrate evolutionary reconstructions and understanding of how new functions evolve


Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling

• Took 56 GEBA genomes and compared results vs. 56 randomly sampled new genomes

• Better definition of protein family sequence “patterns”• Greatly improves “comparative” and “evolutionary”

based predictions• Conversion of hypothetical into conserved hypotheticals• Linking distantly related members of protein families• Improved non-homology predictionKostas

MavrommatisNatalia Ivanova

Thanos Lykidis

Nikos Kyrpides

Iain Anderson



Metadata and individual genome papers important


SIGS http://standardsingenomics.org/


http://standardsingenomics.org/index.php/sigen/index

http://standardsingenomics.org/index.php/sigen/index


Improves analysis of genome data from uncultured organisms


Great Plate Count Anomaly

Culturing Microscope

CountCount




CountCount <<<<




CountCount <<<<

DNA


PCR Saves the Day


rRNA Phylotyping• Collect DNA from

environment• PCR amplify rRNA

genes using broad (so-called universal) primers

• Sequence• Align to others• Infer evolutionary tree• Unknowns “identified”

by placement on tree• Some use BLAST, but

not as good as phylogeny62


Uses of rRNA sequences

The Hidden Majority Richness estimates

Bohannan and Hughes 2003

Hugenholtz 2002


rRNA: A Phylogenetic Anchor to Determine Who’s Out There

Eisen et al. 199264



Eisen et al. 199264



Eisen et al. 199264



Eisen et al. 1992

Biology not similar enough 64


Metagenomics

shotgun

clone



Example I: Phylotyping with rRNA and other genes


0

0.1250

0.2500

0.3750

0.5000

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ghte

d %

of C

lone

s

Major Phylogenetic Group

EFGEFTuHSP70RecARpoBrRNA

Shotgun Sequencing Allows Use of Other Markers

Venter et al., 200468


0

0.1250

0.2500

0.3750

0.5000

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ghte

d %

of C

lone

s




Venter et al., 2004

Cannot be done without good sampling of genomes


Example II: Binning


Metagenomics Challenge


ABCDEFG

TUVWXYZ

Binning challenge


Glassy Winged Sharpshooter

• Feeds on xylem sap

• Vector for Pierce’s Disease

• Potential bioterror agent


Xylem and Phloem

From Lodish et al. 2000


Wu et al. 2006 PLoS Biology 4: e188. 75Monday, November 26, 12

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040188


Sharpshooter Shotgun Sequencing

shotgun

Wu et al. 2006 PLoS Biology 4: e188.Collaboration with Nancy Moran’s lab 76




Baumannia is a Vitamin and Cofactor Producing Machine

Wu et al. 2006 PLoS Biology 4: e188. 77









No Amino-Acid Synthesis




???????


Commonly Used Binning MethodsDid not Work Well

• Assembly– Only Baumannia generated good contigs

• Depth of coverage– Everything else 0-1X coverage

• Nucleotide composition– No detectible peaks in any vector we looked at


CFB Phyla


Wu et al. 2006 PLoS Biology 4: e188. 83Monday, November 26, 12



Essential Amino Acid Synthesis

Wu et al. 2006 PLoS Biology 4: e188. 84






Wu et al. 2006 PLoS Biology 4: e188.

Baumannia makes vitamins and cofactors

Sulcia makes amino acids





0

0.1250

0.2500

0.3750

0.5000

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ghte

d %

of C

lone

s




Venter et al., 2004

Cannot be done without good sampling of genomes


0

0.1250

0.2500

0.3750

0.5000

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ghte

d %

of C

lone

s




Venter et al., 2004

GEBA Project improves metagenomic analysis, but only a little


GEBA Future 1

Need to adapt genomic and metagenomic methods to make use of

GEBA data


Ways to Make Better Use of GEBA Data

• Better phylogenetic methods for short reads• Rebuild protein family models• Need better phylogenies, including HGT• Improved tools for using distantly related

genomes in metagenomic analysis


GEBA Future 2

Need Experiments from Across the Tree of Life too


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Experimental studies are mostly from three phyla

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Experimental studies are mostly from three phyla

• Some studies in other phyla

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Eukaryotes

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Viruses

As of 2002



0.1

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

Tree based on Hugenholtz (2002) with some modifications.

Need experimental studies from across the tree too


0.1

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

Tree based on Hugenholtz (2002) with some modifications.

Adopt a Microbe


GEBA Future 3

We have still only scratched the surface of microbial diversity


rRNA Tree of Life

Based on tree by

Norm Pace


Phylogenetic Diversity: Sequenced Bacteria & Archaea


Phylogenetic Diversity with GEBA


Phylogenetic Diversity: Isolates


Phylogenetic Diversity: All


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter



• Most phyla with cultured species are sparsely sampled

• Lineages with no cultured taxa even more poorly sampled

Well sampled phylaPoorly sampledNo cultured taxa 105


Uncultured Lineages:Technical Approaches

• Get into culture• Enrichment cultures• If abundant in low diversity ecosystems• Flow sorting• Microbeads• Microfluidic sorting• Single cell amplification


Conclusion

• Phylogenetic sampling of genomes improves our understanding of microbial diversity in many ways

• Still need– More biogeography– More phenotypic/experimental data– Deeper phylogenetic sampling



MICROBES


A Happy Tree of Life


Health & Medicine

Phylogenomics and the diversity and the diversification of microbes